If you want to choose the File registration method, you need to activate the following properties via MST or Command Line, and you also need to precopy the license file to a directory that can be reached at run time. I copied our license file onto the users pc before installation via a WiseScript
BABLICENSESOURCE = File
BABCODEFILE = C:\Windows\AELogs\Babylon\NameOfLicenseFile.bof
If you don't have a full path along with file name, you will get the following error.
Setup Type: Windows Installer (MSI)
Deployment Method Used: Windows Installer with Custom Transform (MST)